# HG changeset patch
# User urgi-team
# Date 1450175736 18000
# Node ID a6b557df86db3452daa78e293ae3c4bffdb987a0
# Parent 7557b71a92e702a4eeef9aa9075e5e8a3f5ece45
Uploaded
diff -r 7557b71a92e7 -r a6b557df86db Galaxy-Workflow-workflow_gandalf_1_set.ga
--- a/Galaxy-Workflow-workflow_gandalf_1_set.ga Wed Nov 25 09:34:17 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,384 +0,0 @@
-{
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\ No newline at end of file
diff -r 7557b71a92e7 -r a6b557df86db Galaxy-Workflow-workflow_gandalf_2_sets.ga
--- a/Galaxy-Workflow-workflow_gandalf_2_sets.ga Wed Nov 25 09:34:17 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,933 +0,0 @@
-{
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- "left": 1642,
- "top": 1770
- },
- "post_job_actions": {
- "HideDatasetActionoutput1": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "output1"
- },
- "RenameDatasetActionoutput1": {
- "action_arguments": {
- "newname": "#{inupt1| basename}.stats"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "output1"
- }
- },
- "tool_errors": null,
- "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.1",
- "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\"}",
- "tool_version": "1.0.1",
- "type": "tool",
- "user_outputs": []
- },
- "16": {
- "annotation": "",
- "id": 16,
- "input_connections": {
- "BedFile_List|BedFiles_0|inputBed": {
- "id": 5,
- "output_name": "output_bed"
- },
- "inputVCF": {
- "id": 12,
- "output_name": "output_vcf_firstBAM"
- }
- },
- "inputs": [],
- "name": "VCFFiltering",
- "outputs": [
- {
- "name": "outputVCF",
- "type": "vcf"
- },
- {
- "name": "output_html",
- "type": "html"
- }
- ],
- "position": {
- "left": 1970,
- "top": 593
- },
- "post_job_actions": {
- "HideDatasetActionoutputVCF": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "outputVCF"
- },
- "HideDatasetActionoutput_html": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "output_html"
- },
- "RenameDatasetActionoutputVCF": {
- "action_arguments": {
- "newname": "#{inputVCF | basename}.filteredVCF"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "outputVCF"
- },
- "RenameDatasetActionoutput_html": {
- "action_arguments": {
- "newname": "#{inputVCF | basename}.VCFFiltering.graphs"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "output_html"
- }
- },
- "tool_errors": null,
- "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01",
- "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"BedFiles\\\": [{\\\"__index__\\\": 0, \\\"inputBed\\\": null}], \\\"is_BedFile\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"519bd5da87bc11e5aa509e87638b9e35\\\"\", \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
- "tool_version": "0.01",
- "type": "tool",
- "user_outputs": []
- },
- "17": {
- "annotation": "",
- "id": 17,
- "input_connections": {
- "BedFile_List|BedFiles_0|inputBed": {
- "id": 5,
- "output_name": "output_bed"
- },
- "inputVCF": {
- "id": 14,
- "output_name": "output_vcf_firstBAM"
- }
- },
- "inputs": [],
- "name": "VCFFiltering",
- "outputs": [
- {
- "name": "outputVCF",
- "type": "vcf"
- },
- {
- "name": "output_html",
- "type": "html"
- }
- ],
- "position": {
- "left": 1970,
- "top": 778
- },
- "post_job_actions": {
- "HideDatasetActionoutputVCF": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "outputVCF"
- },
- "HideDatasetActionoutput_html": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "output_html"
- },
- "RenameDatasetActionoutputVCF": {
- "action_arguments": {
- "newname": "#{inputVCF | basename}.filteredVCF"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "outputVCF"
- },
- "RenameDatasetActionoutput_html": {
- "action_arguments": {
- "newname": "#{inputVCF | basename}.VCFFiltering.graphs"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "output_html"
- }
- },
- "tool_errors": null,
- "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01",
- "tool_state": "{\"inputVCF\": \"null\", \"BedFile_List\": \"{\\\"BedFiles\\\": [{\\\"__index__\\\": 0, \\\"inputBed\\\": null}], \\\"is_BedFile\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"AF\": \"\\\"0.9\\\"\", \"__page__\": 0, \"DP_auto\": \"{\\\"is_DP_auto\\\": \\\"True\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"6333a3ae87bc11e591529e87638b9e35\\\"\", \"AN\": \"\\\"2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
- "tool_version": "0.01",
- "type": "tool",
- "user_outputs": []
- },
- "18": {
- "annotation": "",
- "id": 18,
- "input_connections": {
- "VCFFile_0|inputStrainVCF": {
- "id": 16,
- "output_name": "outputVCF"
- },
- "VCFFile_1|inputStrainVCF": {
- "id": 17,
- "output_name": "outputVCF"
- },
- "inputFasta": {
- "id": 0,
- "output_name": "output"
- }
- },
- "inputs": [],
- "name": "VCFStorage",
- "outputs": [
- {
- "name": "outputVCFStorage",
- "type": "tabular"
- }
- ],
- "position": {
- "left": 2298,
- "top": 593
- },
- "post_job_actions": {
- "HideDatasetActionoutputVCFStorage": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "outputVCFStorage"
- },
- "RenameDatasetActionoutputVCFStorage": {
- "action_arguments": {
- "newname": "#{inputFasta | basename}.matrix"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "outputVCFStorage"
- }
- },
- "tool_errors": null,
- "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFStorage/0.01",
- "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"VCFFile\": \"[{\\\"strainName\\\": \\\"strain1\\\", \\\"__index__\\\": 0, \\\"inputStrainVCF\\\": null}, {\\\"strainName\\\": \\\"strain2\\\", \\\"__index__\\\": 1, \\\"inputStrainVCF\\\": null}]\", \"inputFasta\": \"null\"}",
- "tool_version": "0.01",
- "type": "tool",
- "user_outputs": []
- },
- "19": {
- "annotation": "",
- "id": 19,
- "input_connections": {
- "inputTabular": {
- "id": 18,
- "output_name": "outputVCFStorage"
- }
- },
- "inputs": [],
- "name": "VCFCarto",
- "outputs": [
- {
- "name": "outputVCFCarto",
- "type": "tabular"
- },
- {
- "name": "output_html",
- "type": "html"
- },
- {
- "name": "output_bed",
- "type": "bed"
- }
- ],
- "position": {
- "left": 2618,
- "top": 593
- },
- "post_job_actions": {
- "HideDatasetActionoutput_bed": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "output_bed"
- },
- "HideDatasetActionoutput_html": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "output_html"
- },
- "RenameDatasetActionoutputVCFCarto": {
- "action_arguments": {
- "newname": "#{inputTabular | basename}.red"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "outputVCFCarto"
- }
- },
- "tool_errors": null,
- "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFCarto/0.01",
- "tool_state": "{\"__page__\": 0, \"parentA\": \"\\\"strain1\\\"\", \"__rerun_remap_job_id__\": null, \"outputType\": \"\\\"raw\\\"\", \"parentH\": \"\\\"strain2\\\"\", \"chromInfo\": \"\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputTabular\": \"null\"}",
- "tool_version": "0.01",
- "type": "tool",
- "user_outputs": []
- }
- },
- "uuid": "f217cc60-5c89-442b-80ee-3d055e407367"
-}
\ No newline at end of file
diff -r 7557b71a92e7 -r a6b557df86db VCFCarto_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/VCFCarto_wrapper.py Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,107 @@
+#!/usr/bin/env python
+
+
+import subprocess, tempfile, sys, os, glob, shutil, time
+from optparse import OptionParser
+
+
+class VCFCartoWrapper(object):
+
+ def __init__(self):
+ self._options = None
+
+
+ def stop_err(self, msg ):
+ sys.stderr.write( "%s\n" % msg )
+ sys.exit()
+
+
+ def setAttributesFromCmdLine(self):
+ description = "VCFcarto can convert your tabulated file into a file with only the SNP from refA and refH.\n"
+ description += "2 formats are possible, either the input format is conserved, or the format is changed into a 3 letter format\n"
+ description += "(\"A\" for refA, \"H\" for refH and \"-\" when the base do not correspond to any parent)\n\n"
+ description += "example 1 : VCFcarto.py -f Storage.out -A G15 -H G23 -o FilteredStorage.out\n"
+ description += "example 2 : VCFcarto.py -f Storage.out -A ref1 -H ref2 -p -s -g -m -o cartoTable.out\n"
+ parser = OptionParser(description = description, version = "0.1")
+ parser.add_option("-f", "--file", dest = "tableName", action = "store", type = "string", help = "Input TSV File name [compulsory] [format: TSV]", default = "")
+ parser.add_option("-o", "--output", dest = "outFile", action = "store", type = "string", help = "output TSV File name [compulsory] [format: TSV]", default = "")
+ parser.add_option("-A", "--refA", dest = "refA", action = "store", type = "string", help = "name of the reference genome A [compulsory] ", default = "")
+ parser.add_option("-H", "--refH", dest = "refH", action = "store", type = "string", help = "name of the reference genome H [compulsory] ", default = "")
+ parser.add_option("-p", "--onlyParents", dest = "onlyPar", action = "store_true", help = "Will change every letters by either A or H depending on which parents the strain correspond to for that base[optional] [default: False]", default = False)
+ parser.add_option("-m", "--mergeMarkers", dest = "mergeMarkers", action = "store_true", help = "Will merge sequential markers with the same information ; option -p is needed [optional] [default: False]", default = False)
+ parser.add_option("-M", "--mergeFile", dest = "mergeFile", action = "store", type = "string", help = "name for the mergeFile ", default = "")
+ parser.add_option("-g", "--graphics", dest = "graphs", action = "store_true", help = "create graphs. Only works with -p[optional] [default: False]", default = False)
+ parser.add_option("-G", "--graphHTML", dest = "graphHTML", action = "store", type = "string", help = "name of the HTML linking to graphs ", default = "")
+ parser.add_option("-d", "--dirGraphs", dest = "dirGraphs", action = "store", type = "string", help = "name of the folder containing graphs ", default = "")
+ options = parser.parse_args()[0]
+ self._setAttributesFromOptions(options)
+
+
+ def _setAttributesFromOptions(self, options):
+ self._options = options
+
+ def run(self):
+ prg = "VCFCarto.py"
+ args = ""
+ args += "-f %s" % self._options.tableName
+ args += " "
+ args += "-o %s" % self._options.outFile
+ args += " "
+ args += "-A %s" % self._options.refA
+ args += " "
+ args += "-H %s" % self._options.refH
+ args += " "
+ args += "-v 2 "
+ if self._options.onlyPar :
+ args += " "
+ args += "-p"
+ if self._options.mergeMarkers :
+ args += " "
+ args += "-m"
+ if self._options.graphs :
+ args += " "
+ args += "-g"
+ cmd = "%s %s" %(prg, args)
+
+ print cmd
+
+ try:
+ tmp_err = tempfile.NamedTemporaryFile().name
+ tmp_stderr = open( tmp_err, 'wb' )
+ proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr )
+ returncode = proc.wait()
+ tmp_stderr.close()
+ # get stderr, allowing for case where it's very large
+ tmp_stderr = open( tmp_err, 'rb' )
+ stderr = ''
+ buffsize = 1048576
+ try:
+ while True:
+ stderr += tmp_stderr.read( buffsize )
+ if not stderr or len( stderr ) % buffsize != 0:
+ break
+ except OverflowError:
+ pass
+ tmp_stderr.close()
+ if stderr:
+ raise Exception, stderr
+ except Exception, e:
+ self.stop_err( 'Error in VCFCarto:\n' + str( e ) )
+
+ if self._options.mergeMarkers :
+ shutil.move("markerList.bed" ,self._options.mergeFile)
+ if self._options.graphs :
+ html = open(self._options.graphHTML, "w")
+
+ os.mkdir(self._options.dirGraphs)
+ lGraphsFiles = glob.glob("VCFCarto_graphs/*")
+ for file in lGraphsFiles :
+ baseName = os.path.basename(file)
+ shutil.move( file ,"%s/%s" %(self._options.dirGraphs, baseName))
+ line = " \n" %(baseName)
+ html.write(line)
+
+if __name__ == "__main__":
+ iWrapper = VCFCartoWrapper()
+ iWrapper.setAttributesFromCmdLine()
+ iWrapper.run()
diff -r 7557b71a92e7 -r a6b557df86db VCFCarto_wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/VCFCarto_wrapper.xml Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,315 @@
+
+ VCFcarto can convert a tabulated marker file into a file with only the markers from 2 parents
+
+ VCF_Gandalf_Tools
+
+
+ VCFCarto.py --version
+
+
+ VCFCarto_wrapper.py -f $inputTabular -o $outputVCFCarto -A $parentA -H $parentH
+ #if str($outputType) == "carto"
+ -p -g --graphHTML $output_html --dirGraphs "$output_html.files_path"
+ #end if
+ #if str($outputType) == "MergedCarto"
+ -p -g --graphHTML $output_html --dirGraphs "$output_html.files_path" -m --mergeFile $output_bed
+ #end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ not outputType == "raw"
+
+
+ outputType == "MergedCarto"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 7557b71a92e7 -r a6b557df86db VCFFiltering_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/VCFFiltering_wrapper.py Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,110 @@
+#!/usr/bin/env python
+
+
+import subprocess, tempfile, sys, os, glob, shutil, time
+from optparse import OptionParser
+from optparse import Option, OptionValueError
+
+class VCFFilteringWrapper(object):
+
+ def __init__(self):
+ self._options = None
+
+
+ def stop_err(self, msg ):
+ sys.stderr.write( "%s\n" % msg )
+ sys.exit()
+
+
+ def setAttributesFromCmdLine(self):
+ description = "VCFFiltering_wrapper"
+ description += "\nWrapper for VCFFiltering ;\n VCFFiltering filters SNP on a VCF depending on depth (DP) allele number (AN), allele frequency (AF) and SNP quality.\n"
+ description += "example 1 : VCFFiltering.py -f myVCF.vcf -o FilteredVCF.vcf\n"
+ description += "example 2 : VCFFiltering.py -f myVCF.vcf -N 2 -F 0.87 -b bed1.bed bed2.bed -o FilteredVCF.vcf\n"
+ parser = OptionParser(description = description, version = "0.1")
+ parser.add_option("-f", "--vcf", dest = "VCFFile", action = "store", type = "string", help = "Input VCF File name [compulsory] [format: VCF]", default = "")
+ parser.add_option("-o", "--output", dest = "outFile", action = "store", type = "string", help = "output VCF File name [compulsory] [format: VCF]", default = "")
+ parser.add_option("-m", "--minDP", dest = "minDP", action = "store", type = "int", help = "minimum of depth ; if both minDP and maxDP are set, optimal DP will not be calculated ", default = 0)
+ parser.add_option("-M", "--maxDP", dest = "maxDP", action = "store", type = "int", help = "maximum of depth ; if both minDP and maxDP are set, optimal DP will not be calculated ", default = 0)
+ parser.add_option("-N", "--AN", dest = "AN", action = "store", type = "int", help = "maximum number of allele for a SNP; default = 2", default = 2)
+ parser.add_option("-F", "--AF", dest = "AF", action = "store", type = "float", help = "minimum frequency for the alternative allele of a SNP; default = 0.9", default = 0.9)
+ parser.add_option("-b", "--bed", dest = "bedFiles", action = "append", type = "string", help = "bed files: list of coordinates to filter, multiple arguments allowed '-b file1 file2' ", default = [])
+ parser.add_option("-G", "--graphHTML", dest = "graphHTML", action = "store", type = "string", help = "name of the HTML linking to graphs ", default = "")
+ parser.add_option("-d", "--dirGraphs", dest = "dirGraphs", action = "store", type = "string", help = "name of the folder containing graphs ", default = "")
+ options = parser.parse_args()[0]
+ self._setAttributesFromOptions(options)
+
+
+ def _setAttributesFromOptions(self, options):
+ self._options = options
+
+ def run(self):
+ if self._options.minDP and self._options.maxDP :
+ if self._options.minDP > self._options.maxDP :
+ self.stop_err( 'error in options : minDP > max DP (%s > %s)' %(self._options.minDP,self._options.maxDP))
+
+ prg = "VCFFiltering.py -g -G 'png' "
+ args = ""
+ args += "-f %s" % self._options.VCFFile
+ args += " "
+ args += "-o %s" % self._options.outFile
+ if self._options.AF :
+ args += " "
+ args += "-F %s" % self._options.AF
+ if self._options.AN :
+ args += " "
+ args += "-N %s" % self._options.AN
+ if self._options.minDP :
+ args += " "
+ args += "-m %s" % self._options.minDP
+ if self._options.maxDP :
+ args += " "
+ args += "-M %s" % self._options.maxDP
+ if self._options.bedFiles :
+ if self._options.bedFiles == "":
+ pass
+ else :
+ self._lBedFiles = self._options.bedFiles
+ cmd = "%s %s" %(prg, args)
+
+ print cmd
+
+ try:
+ tmp_err = tempfile.NamedTemporaryFile().name
+ tmp_stderr = open( tmp_err, 'wb' )
+ proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr )
+ returncode = proc.wait()
+ tmp_stderr.close()
+ # get stderr, allowing for case where it's very large
+ tmp_stderr = open( tmp_err, 'rb' )
+ stderr = ''
+ buffsize = 1048576
+ try:
+ while True:
+ stderr += tmp_stderr.read( buffsize )
+ if not stderr or len( stderr ) % buffsize != 0:
+ break
+ except OverflowError:
+ pass
+ tmp_stderr.close()
+ if stderr:
+ raise Exception, stderr
+ except Exception, e:
+ self.stop_err( 'Error in VCFFiltering:\n' + str( e ) )
+
+ if True :
+ html = open(self._options.graphHTML, "w")
+
+ os.mkdir(self._options.dirGraphs)
+ lGraphsFiles = glob.glob("VCFFiltering_graphs/*")
+ for file in lGraphsFiles :
+ baseName = os.path.basename(file)
+ shutil.move( file ,"%s/%s" %(self._options.dirGraphs, baseName))
+ line = " \n" %(baseName)
+ html.write(line)
+
+
+if __name__ == "__main__":
+ iWrapper = VCFFilteringWrapper()
+ iWrapper.setAttributesFromCmdLine()
+ iWrapper.run()
diff -r 7557b71a92e7 -r a6b557df86db VCFFiltering_wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/VCFFiltering_wrapper.xml Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,157 @@
+
+ Filters SNP on a VCF depending on depth, allele number and allele frequency
+
+ VCF_Gandalf_Tools
+
+
+ VCFFiltering.py --version
+
+
+ #if $DP_auto.is_DP_auto
+ VCFFiltering_wrapper.py -f $inputVCF -o $outputVCF -F $AF -N $AN
+ #else
+ VCFFiltering_wrapper.py -f $inputVCF -o $outputVCF -F $AF -N $AN -m $DP_auto.DPmin -M $DP_auto.DPmax
+ #end if
+ ## Bed files
+ #if $BedFile_List.is_BedFile
+ #for $bed in $BedFile_List.BedFiles
+ -b $bed.inputBed
+ #end for
+ #end if
+ --graphHTML $output_html --dirGraphs "$output_html.files_path"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 7557b71a92e7 -r a6b557df86db VCFStorage_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/VCFStorage_wrapper.py Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,96 @@
+#!/usr/bin/env python
+
+
+import subprocess, tempfile, sys, os, glob, shutil, time, random
+from optparse import OptionParser
+from optparse import Option, OptionValueError
+
+class VCFStorageWrapper(object):
+
+ def __init__(self):
+ self._options = None
+
+
+ def stop_err(self, msg ):
+ sys.stderr.write( "%s\n" % msg )
+ sys.exit()
+
+
+ def setAttributesFromCmdLine(self):
+ description = "VCFStorage_wrapper"
+ description += "\nWrapper for VCFStorage\n VCFStorage "
+ description += "VCFStorage stores info from variant calling into a table. It will create a tabulate file with the different infos\n"
+ description += "example : VCFStorage -f fasta.fa -l genomelist.list -w workdir -o output.tab \n"
+ parser = OptionParser(description = description, version = "0.1")
+ parser.add_option("-f", "--fasta", dest = "fastaFile", action = "store", type = "string", help = "Input fasta file name [compulsory] [format: Fasta]", default = "")
+ parser.add_option("-l", "--genomeNameList", dest = "genomeNameList", action = "append", type = "string", help = "Input list of genome name ")
+ parser.add_option("-L", "--genomeFileList", dest = "genomeFileList", action = "append", type = "string", help = "Input list of genome VCF file ")
+ parser.add_option("-w", "--workDir", dest = "workDir", action = "store", type = "string", help = "name of the workingDirectory", default = "")
+ parser.add_option("-o", "--out", dest = "outFile", action = "store", type = "string", help = "Output file name [compulsory] [format: tab]", default = "")
+ options = parser.parse_args()[0]
+ self._setAttributesFromOptions(options)
+
+
+ def _setAttributesFromOptions(self, options):
+ self._options = options
+
+ def run(self):
+ self.createGenomeList()
+ cmd = self.createCmdLine()
+ self.launchCmdLine(cmd)
+
+ def createGenomeList(self):
+ self.genomelistFile = "%s.genomeListFile" % self._options.outFile
+ lGenomeName = self._options.genomeNameList
+ lGenomeVCF = self._options.genomeFileList
+ output = open(self.genomelistFile, "w")
+ for i,genomeName in enumerate(lGenomeName) :
+ output.write("%s\t%s\n" % (lGenomeName[i],lGenomeVCF[i]))
+ output.close()
+
+ def createCmdLine(self):
+ workdir = "VCFStorage_%s_%d" % (time.strftime("%d%H%M%S"), random.randint(0, 10000))
+ prg = "VCFStorage.py"
+ args = ""
+ args += "-f %s" % self._options.fastaFile
+ args += " "
+ args += "-o %s" % self._options.outFile
+ args += " "
+ args += "-l %s" % self.genomelistFile
+ args += " "
+ args += "-w %s" % workdir
+ cmd = "%s %s" %(prg, args)
+
+ print cmd
+ return cmd
+
+ def launchCmdLine(self, cmd):
+ try:
+ tmp_err = tempfile.NamedTemporaryFile().name
+ tmp_stderr = open( tmp_err, 'wb' )
+ proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr )
+ returncode = proc.wait()
+ tmp_stderr.close()
+ # get stderr, allowing for case where it's very large
+ tmp_stderr = open( tmp_err, 'rb' )
+ stderr = ''
+ buffsize = 1048576
+ try:
+ while True:
+ stderr += tmp_stderr.read( buffsize )
+ if not stderr or len( stderr ) % buffsize != 0:
+ break
+ except OverflowError:
+ pass
+ tmp_stderr.close()
+ if stderr:
+ raise Exception, stderr
+ except Exception, e:
+ os.remove(self.genomelistFile)
+ self.stop_err( 'Error in VCFStorage:\n' + str( e ) )
+ os.remove(self.genomelistFile)
+
+if __name__ == "__main__":
+ iWrapper = VCFStorageWrapper()
+ iWrapper.setAttributesFromCmdLine()
+ iWrapper.run()
diff -r 7557b71a92e7 -r a6b557df86db VCFStorage_wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/VCFStorage_wrapper.xml Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,236 @@
+
+ stores info from variant calling into a table. It will create a tabulate filed with SNP infos
+
+ VCF_Gandalf_Tools
+
+
+ VCFStorage.py --version
+
+
+ VCFStorage_wrapper.py -f $inputFasta -o $outputVCFStorage
+ ## genome list
+ #for $VCF in $VCFFile
+ -l $VCF.strainName
+ -L $VCF.inputStrainVCF
+ #end for
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ chr_17
+ ccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaa
+ TACGCGCGCGCCTAACCCTACGACTTTAACCTACTCTAAACTCTCCTACTAGTACGTCTT
+
+VCF input file : ::
+
+ ##fileformat=VCFv4.1
+ ##fileDate=20140725
+ ##source=freeBayes v0.9.13-2-ga830efd
+ ##reference=exmple.fsa
+ ##phasing=none
+ ##DetectedFormat=freebayes
+ ##FILTER=
+ ##FILTER=
+ ##FILTER=
+ ##FILTER=
+ ##FILTER=
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT V1
+ chr_17 17 . A G 529.213 G_AF;G_DP AB=0.583333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=21;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.1137;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=77.012;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=751;QR=535;RO=15;RPP=5.59539;RPPR=4.31318;RUN=1;SAF=11;SAP=3.1137;SAR=10;SRF=5;SRP=6.62942;SRR=10;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.58;G_DP=36;G_Base=G GT:DP:RO:QR:AO:QA:GL 0/1:36:15:535:21:751:-10,0,-10
+ chr_17 37 . C G 1082.38 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=34;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=3.26577;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=48.0391;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1243;QR=0;RO=0;RPP=15.5282;RPPR=0;RUN=1;SAF=18;SAP=3.26577;SAR=16;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=34;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:34:0:0:34:1243:-10,-9.23017,0
+ chr_17 40 . T T 825.518 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=29;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=6.67934;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.92992;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1082;QR=178;RO=5;RPP=9.07545;RPPR=13.8677;RUN=1;SAF=13;SAP=3.68421;SAR=16;SRF=5;SRP=13.8677;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.85;G_DP=34;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:34:5:178:29:1082:-10,0,-6.82575
+ chr_17 60 . A . 699.741 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=22;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=17.2236;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=32.2544;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=823;QR=0;RO=0;RPP=9.32731;RPPR=0;RUN=1;SAF=12;SAP=3.40511;SAR=10;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=22;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:22:0:0:22:823:-10,-5.98732,0
+ chr_17 73 . T . 846.299 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=27;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=16.6021;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=38.84;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1002;QR=0;RO=0;RPP=5.02092;RPPR=0;RUN=1;SAF=21;SAP=21.1059;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=27;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:27:0:0:27:1002:-10,-7.34226,0
+ chr_17 81 . C T 764.464 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=25;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=13.5202;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=36.1324;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=902;QR=0;RO=0;RPP=3.79203;RPPR=0;RUN=1;SAF=19;SAP=17.6895;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=25;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:25:0:0:25:902:-10,-6.76842,0
+ chr_17 105 . C T 1154 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=37;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.88603;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=52.0047;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1336;QR=0;RO=0;RPP=19.9713;RPPR=0;RUN=1;SAF=23;SAP=7.76406;SAR=14;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=37;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:37:0:0:37:1336:-10,-10,0
+ chr_17 112 . G A 1276.25 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=40;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=10.8276;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=55.9501;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1471;QR=0;RO=0;RPP=10.8276;RPPR=0;RUN=1;SAF=26;SAP=10.8276;SAR=14;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=40;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:40:0:0:40:1471:-10,-10,0
+
+expected result : ::
+
+ CHROM POS reference V1
+ chr_17 1 C U
+ chr_17 2 C U
+ chr_17 3 C U
+ chr_17 4 T U
+ chr_17 5 A U
+ chr_17 6 A U
+ chr_17 7 C U
+ chr_17 8 C U
+ chr_17 9 C U
+ chr_17 10 T U
+ chr_17 11 A U
+ chr_17 12 A U
+ chr_17 13 C U
+ chr_17 14 C U
+ chr_17 15 C U
+ chr_17 16 T U
+ chr_17 17 A F
+ chr_17 18 A U
+ chr_17 19 C U
+ chr_17 20 C U
+ chr_17 21 C U
+ chr_17 22 T U
+ chr_17 23 A U
+ chr_17 24 A U
+ chr_17 25 C U
+ chr_17 26 C U
+ chr_17 27 C U
+ chr_17 28 T U
+ chr_17 29 A U
+ chr_17 30 A U
+ chr_17 31 C U
+ chr_17 32 C U
+ chr_17 33 C U
+ chr_17 34 T U
+ chr_17 35 A U
+ chr_17 36 A U
+ chr_17 37 C G
+ chr_17 38 C U
+ chr_17 39 C U
+ chr_17 40 T F
+ chr_17 41 A U
+ chr_17 42 A U
+ chr_17 43 C U
+ chr_17 44 C U
+ chr_17 45 C U
+ chr_17 46 T U
+ chr_17 47 A U
+ chr_17 48 A U
+ chr_17 49 C U
+ chr_17 50 C U
+ chr_17 51 C U
+ chr_17 52 T U
+ chr_17 53 A U
+ chr_17 54 A U
+ chr_17 55 C U
+ chr_17 56 C U
+ chr_17 57 C U
+ chr_17 58 T U
+ chr_17 59 A U
+ chr_17 60 A R
+ chr_17 61 T U
+ chr_17 62 A U
+ chr_17 63 C U
+ chr_17 64 G U
+ chr_17 65 C U
+ chr_17 66 G U
+ chr_17 67 C U
+ chr_17 68 G U
+ chr_17 69 C U
+ chr_17 70 G U
+ chr_17 71 C U
+ chr_17 72 C U
+ chr_17 73 T R
+ chr_17 74 A U
+ chr_17 75 A U
+ chr_17 76 C U
+ chr_17 77 C U
+ chr_17 78 C U
+ chr_17 79 T U
+ chr_17 80 A U
+ chr_17 81 C T
+ chr_17 82 G U
+ chr_17 83 A U
+ chr_17 84 C U
+ chr_17 85 T U
+ chr_17 86 T U
+ chr_17 87 T U
+ chr_17 88 A U
+ chr_17 89 A U
+ chr_17 90 C U
+ chr_17 91 C U
+ chr_17 92 T U
+ chr_17 93 A U
+ chr_17 94 C U
+ chr_17 95 T U
+ chr_17 96 C U
+ chr_17 97 T U
+ chr_17 98 A U
+ chr_17 99 A U
+ chr_17 100 A U
+ chr_17 101 C U
+ chr_17 102 T U
+ chr_17 103 C U
+ chr_17 104 T U
+ chr_17 105 C F
+ chr_17 106 C U
+ chr_17 107 T U
+ chr_17 108 A U
+ chr_17 109 C U
+ chr_17 110 T U
+ chr_17 111 A U
+ chr_17 112 G F
+ chr_17 113 T U
+ chr_17 114 A U
+ chr_17 115 C U
+ chr_17 116 G U
+ chr_17 117 T U
+ chr_17 118 C U
+ chr_17 119 T U
+ chr_17 120 T U
+
+-----
+
+**reference :**
+
+]]>
+
+
diff -r 7557b71a92e7 -r a6b557df86db repository_dependencies.xml
--- a/repository_dependencies.xml Wed Nov 25 09:34:17 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-
-
-
-
-
-
-
-
-
-
diff -r 7557b71a92e7 -r a6b557df86db test-data/Expchr17.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Expchr17.tab Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,121 @@
+CHROM POS reference V1
+chr_17 1 C U
+chr_17 2 C U
+chr_17 3 C U
+chr_17 4 T U
+chr_17 5 A U
+chr_17 6 A U
+chr_17 7 C U
+chr_17 8 C U
+chr_17 9 C U
+chr_17 10 T U
+chr_17 11 A U
+chr_17 12 A U
+chr_17 13 C U
+chr_17 14 C U
+chr_17 15 C U
+chr_17 16 T U
+chr_17 17 A F
+chr_17 18 A U
+chr_17 19 C U
+chr_17 20 C U
+chr_17 21 C U
+chr_17 22 T U
+chr_17 23 A U
+chr_17 24 A U
+chr_17 25 C U
+chr_17 26 C U
+chr_17 27 C U
+chr_17 28 T U
+chr_17 29 A U
+chr_17 30 A U
+chr_17 31 C U
+chr_17 32 C U
+chr_17 33 C U
+chr_17 34 T U
+chr_17 35 A U
+chr_17 36 A U
+chr_17 37 C G
+chr_17 38 C U
+chr_17 39 C U
+chr_17 40 T F
+chr_17 41 A U
+chr_17 42 A U
+chr_17 43 C U
+chr_17 44 C U
+chr_17 45 C U
+chr_17 46 T U
+chr_17 47 A U
+chr_17 48 A U
+chr_17 49 C U
+chr_17 50 C U
+chr_17 51 C U
+chr_17 52 T U
+chr_17 53 A U
+chr_17 54 A U
+chr_17 55 C U
+chr_17 56 C U
+chr_17 57 C U
+chr_17 58 T U
+chr_17 59 A U
+chr_17 60 A R
+chr_17 61 T U
+chr_17 62 A U
+chr_17 63 C U
+chr_17 64 G U
+chr_17 65 C U
+chr_17 66 G U
+chr_17 67 C U
+chr_17 68 G U
+chr_17 69 C U
+chr_17 70 G U
+chr_17 71 C U
+chr_17 72 C U
+chr_17 73 T R
+chr_17 74 A U
+chr_17 75 A U
+chr_17 76 C U
+chr_17 77 C U
+chr_17 78 C U
+chr_17 79 T U
+chr_17 80 A U
+chr_17 81 C T
+chr_17 82 G U
+chr_17 83 A U
+chr_17 84 C U
+chr_17 85 T U
+chr_17 86 T U
+chr_17 87 T U
+chr_17 88 A U
+chr_17 89 A U
+chr_17 90 C U
+chr_17 91 C U
+chr_17 92 T U
+chr_17 93 A U
+chr_17 94 C U
+chr_17 95 T U
+chr_17 96 C U
+chr_17 97 T U
+chr_17 98 A U
+chr_17 99 A U
+chr_17 100 A U
+chr_17 101 C U
+chr_17 102 T U
+chr_17 103 C U
+chr_17 104 T U
+chr_17 105 C F
+chr_17 106 C U
+chr_17 107 T U
+chr_17 108 A U
+chr_17 109 C U
+chr_17 110 T U
+chr_17 111 A U
+chr_17 112 G F
+chr_17 113 T U
+chr_17 114 A U
+chr_17 115 C U
+chr_17 116 G U
+chr_17 117 T U
+chr_17 118 C U
+chr_17 119 T U
+chr_17 120 T U
diff -r 7557b71a92e7 -r a6b557df86db test-data/VCFCarto_input.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/VCFCarto_input.tab Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,76 @@
+CHROM POS reference REF1 G01 REF2 G02 G03 G04 G05 G06 G07 G08 G09 G10 G11 G12
+Chr1 1 A R R R R U R R R R R R R R R
+Chr1 2 T R R R R R U R R R R R R R R
+Chr1 3 G R R R R R R R R R R R R R R
+Chr1 4 G R R R R R R R R R R R R F R
+Chr1 5 G R R R R R R U F R R R R R R
+Chr1 6 C R R R R R R R R R R R R R U
+Chr1 7 A G C C C F C C C C C G C G G
+Chr1 8 G R R R R R R R R R R R R R R
+Chr1 9 C R T T R T T T U R T R T T T
+Chr1 10 T R R R R R R R R R R R R R U
+Chr1 11 T R R R R R R R R R R R F R R
+Chr1 12 A R R R R U R R R R F R R R R
+Chr1 13 A R R G G R F R F G R G R R F
+Chr1 14 A R R R R R R R R F R R R R R
+Chr1 15 G R R R U R F R R R R R R U U
+Chr1 16 G A R R A R R U F R R A A R A
+Chr1 17 A R G G R U R R G G R G U R G
+Chr1 18 C R R R R R U R R R R R R R R
+Chr1 19 G C U R C R C U R R C C C R C
+Chr1 20 G A U R A R A U R R A A A R A
+Chr1 21 G T U R T R T U R R T T T R T
+Chr1 22 A T U R T R T U R R T T T R T
+Chr1 23 C T T R T R R R T R U T R T T
+Chr1 24 T R R R R R U R R R R R R R F
+Chr1 25 G R F R R R R R U R F R R R R
+Chr1 26 T R R C C C C C R R C R C R U
+Chr1 27 C R R G G G G R G R G R G R R
+Chr1 28 C G T T T G G T T F T G T T G
+Chr1 29 G T R R R R T R T R T T R T R
+Chr1 30 T R R R R R R R R R R R R R R
+Chr1 31 A R R R R F R R R R F R R R R
+Chr1 32 A G G R G G G R R G G G G G R
+Chr1 33 G R R R R R R R R R R R R R R
+Chr1 34 C R R R R R R R R R R R R R R
+Chr1 35 C R R R R R F R R R R R R R U
+Chr2 1 T R R R F R R R R R R R R R R
+Chr2 2 A C R R C C U R R R R C C C U
+Chr2 3 C R R R R R R U R R R R R R R
+Chr2 4 C R R R R R R R U R R R R F R
+Chr2 5 T R R R R R R R R R R R R R R
+Chr2 6 C R R R R R R R R R R R R R R
+Chr2 7 A T F R U R T T T R T T F T T
+Chr2 8 T R R R R R R R R R R R R R R
+Chr2 9 C R R R R R R R R R R R R R R
+Chr2 10 G R T T T T R T R R R R R U R
+Chr2 11 C R A A A A R A R R R R R U R
+Chr2 12 A R T T T T R T R R R R R U R
+Chr2 13 T R C C C C R C R R R R R U R
+Chr2 14 C T A A T A T A T A T T A A A
+Chr2 15 T R R R F R R R R R R R R R R
+Chr2 16 A R R R R R R R U R R R R R R
+Chr2 17 A R U R R R R R R R R R R R F
+Chr2 18 G R R R R R R R R R R R R R R
+Chr2 19 A R R R R R R F R R R R R R R
+Chr2 20 C R R R R R R R F R R R R R R
+Chr2 21 G A R R A A A R R R A A R R R
+Chr2 22 A R R R R R R F R R R R R R R
+Chr2 23 A R R T T R R T T T T T R R R
+Chr2 24 T R R R R R R U R R R R R R F
+Chr2 25 T R A A R R A R A R R A R R A
+Chr2 26 G R R R R R R R R R R R R R R
+Chr2 27 A R R R R R R R R R R R R U R
+Chr2 28 C R U R R F F R R F R F U R R
+Chr2 29 G R R R R R R F R R R R R R R
+Chr2 30 T A A G A G G A A G F G G G U
+Chr2 31 A R R R R R R R R U U R R R R
+Chr2 32 G R R R R R R U U R R R R R R
+Chr2 33 G R U R R R R U R R R R R R R
+Chr2 34 A R R R U R R R R R R R R R R
+Chr2 35 G R R R R R R R R R R R R R R
+Chr2 36 T R R R R R R U R R R R R R R
+Chr3 1 T U R R R R R U R R R R R R R
+Chr3 2 T R R U R R R U R R R R R R R
+Chr3 3 T F R R R R R U R R R R R R R
+Chr3 4 T R R F R R R U R R R R R R R
diff -r 7557b71a92e7 -r a6b557df86db test-data/VCFCarto_output.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/VCFCarto_output.tab Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,27 @@
+CHROM POS reference REF1 G01 REF2 G02 G03 G04 G05 G06 G07 G08 G09 G10 G11 G12
+Chr1 7 A G C C C F C C C C C G C G G
+Chr1 9 C R T T R T T T U R T R T T T
+Chr1 13 A R R G G R F R F G R G R R F
+Chr1 16 G A R R A R R U F R R A A R A
+Chr1 17 A R G G R U R R G G R G U R G
+Chr1 19 G C U R C R C U R R C C C R C
+Chr1 20 G A U R A R A U R R A A A R A
+Chr1 21 G T U R T R T U R R T T T R T
+Chr1 22 A T U R T R T U R R T T T R T
+Chr1 23 C T T R T R R R T R U T R T T
+Chr1 26 T R R C C C C C R R C R C R U
+Chr1 27 C R R G G G G R G R G R G R R
+Chr1 28 C G T T T G G T T F T G T T G
+Chr1 29 G T R R R R T R T R T T R T R
+Chr1 32 A G G R G G G R R G G G G G R
+Chr2 2 A C R R C C U R R R R C C C U
+Chr2 7 A T F R U R T T T R T T F T T
+Chr2 10 G R T T T T R T R R R R R U R
+Chr2 11 C R A A A A R A R R R R R U R
+Chr2 12 A R T T T T R T R R R R R U R
+Chr2 13 T R C C C C R C R R R R R U R
+Chr2 14 C T A A T A T A T A T T A A A
+Chr2 21 G A R R A A A R R R A A R R R
+Chr2 23 A R R T T R R T T T T T R R R
+Chr2 25 T R A A R R A R A R R A R R A
+Chr2 30 T A A G A G G A A G F G G G U
diff -r 7557b71a92e7 -r a6b557df86db test-data/VCFCarto_output_merged.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/VCFCarto_output_merged.bed Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,20 @@
+Chr1 7 7 *M_00001
+Chr1 9 9 *M_00002
+Chr1 13 13 *M_00003
+Chr1 16 16 *M_00004
+Chr1 17 17 *M_00005
+Chr1 19 22 *M_00006
+Chr1 23 23 *M_00007
+Chr1 26 26 *M_00008
+Chr1 27 27 *M_00009
+Chr1 28 28 *M_00010
+Chr1 29 29 *M_00011
+Chr1 32 32 *M_00012
+Chr2 2 2 *M_00013
+Chr2 7 7 *M_00014
+Chr2 10 13 *M_00015
+Chr2 14 14 *M_00016
+Chr2 21 21 *M_00017
+Chr2 23 23 *M_00018
+Chr2 25 25 *M_00019
+Chr2 30 30 *M_00020
diff -r 7557b71a92e7 -r a6b557df86db test-data/VCFCarto_output_merged.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/VCFCarto_output_merged.tab Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,21 @@
+CHROM POS reference REF1 G01 REF2 G02 G03 G04 G05 G06 G07 G08 G09 G10 G11 G12
+Chr1 *M_00001 - A H H H - H H H H H A H A A
+Chr1 *M_00002 - A H H A H H H - A H A H H H
+Chr1 *M_00003 - A A H H A - A - H A H A A -
+Chr1 *M_00004 - A H H A H H - - H H A A H A
+Chr1 *M_00005 - A H H A - A A H H A H - A H
+Chr1 *M_00006 - A - H A H A - H H A A A H A
+Chr1 *M_00007 - A A H A H H H A H - A H A A
+Chr1 *M_00008 - A A H H H H H A A H A H A -
+Chr1 *M_00009 - A A H H H H A H A H A H A A
+Chr1 *M_00010 - A H H H A A H H - H A H H A
+Chr1 *M_00011 - A H H H H A H A H A A H A H
+Chr1 *M_00012 - A A H A A A H H A A A A A H
+Chr2 *M_00013 - A H H A A - H H H H A A A -
+Chr2 *M_00014 - A - H - H A A A H A A - A A
+Chr2 *M_00015 - A H H H H A H A A A A A - A
+Chr2 *M_00016 - A H H A H A H A H A A H H H
+Chr2 *M_00017 - A H H A A A H H H A A H H H
+Chr2 *M_00018 - A A H H A A H H H H H A A A
+Chr2 *M_00019 - A H H A A H A H A A H A A H
+Chr2 *M_00020 - A A H A H H A A H - H H H -
diff -r 7557b71a92e7 -r a6b557df86db test-data/VCFFiltering_DP_4_200_output.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/VCFFiltering_DP_4_200_output.vcf Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,110 @@
+##fileformat=VCFv4.1
+##fileDate=20140725
+##source=freeBayes v0.9.13-2-ga830efd
+##phasing=none
+##DetectedFormat=freebayes
+##FILTER=
+##FILTER=
+##FILTER=
+##FILTER=
+##FILTER=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G15_myco
+chr_1 235 . C T 21.392 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865778;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:77:-4.63556,0,-2.351
+chr_1 244 . C T 21.1881 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865718;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-4.61503,0,-2.35102
+chr_1 253 . T C 73.475 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=7.23646;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-8.62509,-0.841726,0
+chr_1 333 . G A 24.2337 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=3.07477;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=82;QR=24;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:24:2:82:-4.69685,0,-1.39164
+chr_1 354 . G A 20.5104 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=2.23682;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=28;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:28:2:78:-4.66174,0,-1.75556
+chr_1 363 . G A 40.3032 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36;MQMR=0;NS=1;NUMALT=1;ODDS=5.91856;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:63:-5.23324,-0.570398,0
+chr_1 1531 . G A 73.2764 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=0;NS=1;NUMALT=1;ODDS=7.23732;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=115;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:115:-9.08235,-0.842098,0
+chr_1 1565 . A G 14.5726 G_AF AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=38;MQMR=35;NS=1;NUMALT=1;ODDS=3.30493;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=71;RO=2;RPP=7.35324;RPPR=3.0103;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.50;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 0/1:4:2:71:2:71:-5.0654,0,-4.84835
+chr_1 1589 . A G 102.964 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55461;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=155;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:155:-10,-1.11316,0
+chr_1 1635 . G A 95.7333 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=38.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55365;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=141;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:141:-10,-1.11274,0
+chr_1 2624 . C T 122.967 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=44.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.5553;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=156;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:156:-10,-1.11346,0
+chr_1 2670 . C T 30.7231 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.739044;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:71:-5.60946,0,-2.40604
+chr_1 2671 . G A 30.0349 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.738983;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:70:-5.5406,0,-2.40606
+chr_1 2686 . A G 28.1218 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.861385;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=39;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:3:1:39:2:67:-5.31237,0,-2.3529
+chr_1 2697 . G A 66.8365 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23789;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=104;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:104:-9.39261,-0.842345,0
+chr_1 2699 . G A 75.6507 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23781;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=103;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:103:-9.31979,-0.842311,0
+chr_1 2747 . C T 52.6764 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=5.92179;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=81;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:81:-7.07265,-0.5718,0
+chr_1 3616 . C T 96.527 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55506;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=153;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:153:-10,-1.11336,0
+chr_1 3624 . A G 99.7577 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55532;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=158;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:158:-10,-1.11347,0
+chr_1 3630 . G A 119.888 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=13.8677;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87182;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=191;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:191:-10,-1.38419,0
+chr_1 3657 . T C 146.729 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87224;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:204:-10,-1.38437,0
+chr_1 3681 . C T 141.607 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=8.80089;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=11.1867;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=201;QR=0;RO=0;RPP=8.80089;RPPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:201:-10,-1.65422,0
+chr_1 3746 . G A 143.027 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=177;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:177:-10,-1.38398,0
+chr_1 3766 . TGG TG 207.378 InDel AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1M1D1M;DP=7;DPB=4.66667;DPRA=0;EPP=3.32051;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8571;MQMR=0;NS=1;NUMALT=1;ODDS=12.5052;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=267;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=1;SAP=10.7656;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=del;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=7;G_Base=TG GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:267:-10,-1.9258,0
+chr_1 3804 . C T 168.638 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.1667;MQMR=0;NS=1;NUMALT=1;ODDS=11.188;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=213;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=8.80089;SAR=5;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:213:-10,-1.65476,0
+chr_1 3845 . G A 130.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87163;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=184;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=1;SAP=6.91895;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:184:-10,-1.38411,0
+chr_1 3857 . G A 72.7109 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23836;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=113;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:113:-9.98004,-0.84255,0
+chr_1 4299 . C T 48.7928 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=48;NS=1;NUMALT=1;ODDS=2.04069;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=34;RO=1;RPP=9.52472;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.75;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:1:34:3:100:-7.69498,0,-2.01683
+chr_1 4311 . A G 138.174 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.8711;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=179;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=3;SAP=3.44459;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:179:-10,-1.38387,0
+chr_1 4357 . C T 141.385 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.87061;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=181;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:181:-10,-1.38366,0
+chr_1 4372 . C T 57.8383 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=48;NS=1;NUMALT=1;ODDS=0.86483;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=40;RO=1;RPP=3.73412;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.75;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:1:40:3:110:-8.53351,0,-2.5275
+chr_1 4389 . C T 176.339 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.80219;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=48;NS=1;NUMALT=1;ODDS=6.11702;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=247;QR=37;RO=1;RPP=3.32051;RPPR=5.18177;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.88;G_DP=8;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:8:1:37:7:247:-10,0,-1.14959
+chr_1 4398 . T C 197.868 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.80219;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=0;NS=1;NUMALT=1;ODDS=12.5039;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=243;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=7;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:243:-10,-1.92523,0
+chr_1 4404 . T C 168.543 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=46.3333;MQMR=0;NS=1;NUMALT=1;ODDS=11.1873;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=209;QR=0;RO=0;RPP=4.45795;RPPR=0;RUN=1;SAF=2;SAP=4.45795;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:209:-10,-1.65448,0
+chr_1 4475 . C T 81.0612 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=47;MQMR=0;NS=1;NUMALT=1;ODDS=7.2379;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.86084,-0.842352,0
+chr_1 4540 . C T 72.5101 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23698;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=101;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:101:-9.00573,-0.841952,0
+chr_1 4580 . C T 81.3345 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23817;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=119;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:119:-9.88816,-0.842465,0
+chr_1 4611 . C G 51.9857 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=5.92133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:69:-6.40152,-0.5716,0
+chr_1 4661 . A G 19.7502 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.834078;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-5.08162,0,-2.36476
+chr_1 4678 . G A 21.951 G_AF;G_DP AB=0.666667;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.136458;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 0/1:3:1:41:2:68:-4.94794,0,-2.78626
+chr_1 4686 . C T 81.6957 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23731;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.44717,-0.842096,0
+chr_1 4699 . G A 103.379 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.55324;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=140;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:140:-10,-1.11256,0
+chr_1 4717 . C T 18.6085 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=34;NS=1;NUMALT=1;ODDS=1.12012;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=40;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:40:2:66:-4.87583,0,-2.24054
+chr_1 4727 . G A 43.4619 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=32;MQMR=0;NS=1;NUMALT=1;ODDS=5.91984;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:66:-5.54913,-0.570955,0
+chr_1 4747 . C T 40.3421 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=5.92045;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:68:-5.83919,-0.571218,0
+chr_1 3305168 . T A,G 280.615 G_AF AB=0.75,0.25;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1;G_AN=2;G_AF=0.75;G_DP=12;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10
+chr_1 3305169 . T A,G 280.615 G_AF AB=0.25,0.75;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1;G_AN=2;G_AF=0.75;G_DP=12;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10
diff -r 7557b71a92e7 -r a6b557df86db test-data/VCFFiltering_DPauto_output.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/VCFFiltering_DPauto_output.vcf Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,110 @@
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+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G15_myco
+chr_1 235 . C T 21.392 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865778;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:77:-4.63556,0,-2.351
+chr_1 244 . C T 21.1881 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865718;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-4.61503,0,-2.35102
+chr_1 253 . T C 73.475 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=7.23646;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-8.62509,-0.841726,0
+chr_1 333 . G A 24.2337 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=3.07477;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=82;QR=24;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:24:2:82:-4.69685,0,-1.39164
+chr_1 354 . G A 20.5104 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=2.23682;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=28;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:28:2:78:-4.66174,0,-1.75556
+chr_1 363 . G A 40.3032 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36;MQMR=0;NS=1;NUMALT=1;ODDS=5.91856;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:63:-5.23324,-0.570398,0
+chr_1 1531 . G A 73.2764 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=0;NS=1;NUMALT=1;ODDS=7.23732;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=115;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:115:-9.08235,-0.842098,0
+chr_1 1565 . A G 14.5726 G_AF AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=38;MQMR=35;NS=1;NUMALT=1;ODDS=3.30493;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=71;RO=2;RPP=7.35324;RPPR=3.0103;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.50;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 0/1:4:2:71:2:71:-5.0654,0,-4.84835
+chr_1 1589 . A G 102.964 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55461;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=155;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:155:-10,-1.11316,0
+chr_1 1635 . G A 95.7333 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=38.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55365;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=141;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:141:-10,-1.11274,0
+chr_1 2624 . C T 122.967 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=44.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.5553;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=156;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:156:-10,-1.11346,0
+chr_1 2670 . C T 30.7231 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.739044;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:71:-5.60946,0,-2.40604
+chr_1 2671 . G A 30.0349 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.738983;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:70:-5.5406,0,-2.40606
+chr_1 2686 . A G 28.1218 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.861385;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=39;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:3:1:39:2:67:-5.31237,0,-2.3529
+chr_1 2697 . G A 66.8365 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23789;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=104;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:104:-9.39261,-0.842345,0
+chr_1 2699 . G A 75.6507 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23781;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=103;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:103:-9.31979,-0.842311,0
+chr_1 2747 . C T 52.6764 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=5.92179;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=81;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:81:-7.07265,-0.5718,0
+chr_1 3616 . C T 96.527 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55506;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=153;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:153:-10,-1.11336,0
+chr_1 3624 . A G 99.7577 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55532;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=158;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:158:-10,-1.11347,0
+chr_1 3630 . G A 119.888 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=13.8677;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87182;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=191;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:191:-10,-1.38419,0
+chr_1 3657 . T C 146.729 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87224;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:204:-10,-1.38437,0
+chr_1 3681 . C T 141.607 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=8.80089;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=11.1867;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=201;QR=0;RO=0;RPP=8.80089;RPPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:201:-10,-1.65422,0
+chr_1 3746 . G A 143.027 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=177;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:177:-10,-1.38398,0
+chr_1 3766 . TGG TG 207.378 InDel;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1M1D1M;DP=7;DPB=4.66667;DPRA=0;EPP=3.32051;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8571;MQMR=0;NS=1;NUMALT=1;ODDS=12.5052;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=267;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=1;SAP=10.7656;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=del;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=7;G_Base=TG GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:267:-10,-1.9258,0
+chr_1 3804 . C T 168.638 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.1667;MQMR=0;NS=1;NUMALT=1;ODDS=11.188;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=213;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=8.80089;SAR=5;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:213:-10,-1.65476,0
+chr_1 3845 . G A 130.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87163;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=184;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=1;SAP=6.91895;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:184:-10,-1.38411,0
+chr_1 3857 . G A 72.7109 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23836;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=113;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:113:-9.98004,-0.84255,0
+chr_1 4299 . C T 48.7928 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=48;NS=1;NUMALT=1;ODDS=2.04069;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=34;RO=1;RPP=9.52472;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.75;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:1:34:3:100:-7.69498,0,-2.01683
+chr_1 4311 . A G 138.174 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.8711;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=179;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=3;SAP=3.44459;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:179:-10,-1.38387,0
+chr_1 4357 . C T 141.385 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.87061;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=181;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:181:-10,-1.38366,0
+chr_1 4372 . C T 57.8383 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=48;NS=1;NUMALT=1;ODDS=0.86483;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=40;RO=1;RPP=3.73412;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.75;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:1:40:3:110:-8.53351,0,-2.5275
+chr_1 4389 . C T 176.339 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.80219;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=48;NS=1;NUMALT=1;ODDS=6.11702;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=247;QR=37;RO=1;RPP=3.32051;RPPR=5.18177;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.88;G_DP=8;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:8:1:37:7:247:-10,0,-1.14959
+chr_1 4398 . T C 197.868 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.80219;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=0;NS=1;NUMALT=1;ODDS=12.5039;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=243;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=7;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:243:-10,-1.92523,0
+chr_1 4404 . T C 168.543 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=46.3333;MQMR=0;NS=1;NUMALT=1;ODDS=11.1873;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=209;QR=0;RO=0;RPP=4.45795;RPPR=0;RUN=1;SAF=2;SAP=4.45795;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:209:-10,-1.65448,0
+chr_1 4475 . C T 81.0612 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=47;MQMR=0;NS=1;NUMALT=1;ODDS=7.2379;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.86084,-0.842352,0
+chr_1 4540 . C T 72.5101 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23698;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=101;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:101:-9.00573,-0.841952,0
+chr_1 4580 . C T 81.3345 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23817;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=119;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:119:-9.88816,-0.842465,0
+chr_1 4611 . C G 51.9857 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=5.92133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:69:-6.40152,-0.5716,0
+chr_1 4661 . A G 19.7502 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.834078;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-5.08162,0,-2.36476
+chr_1 4678 . G A 21.951 G_AF AB=0.666667;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.136458;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 0/1:3:1:41:2:68:-4.94794,0,-2.78626
+chr_1 4686 . C T 81.6957 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23731;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.44717,-0.842096,0
+chr_1 4699 . G A 103.379 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.55324;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=140;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:140:-10,-1.11256,0
+chr_1 4717 . C T 18.6085 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=34;NS=1;NUMALT=1;ODDS=1.12012;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=40;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:40:2:66:-4.87583,0,-2.24054
+chr_1 4727 . G A 43.4619 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=32;MQMR=0;NS=1;NUMALT=1;ODDS=5.91984;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:66:-5.54913,-0.570955,0
+chr_1 4747 . C T 40.3421 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=5.92045;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:68:-5.83919,-0.571218,0
+chr_1 3305168 . T A,G 280.615 G_AF;G_DP AB=0.75,0.25;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1;G_AN=2;G_AF=0.75;G_DP=12;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10
+chr_1 3305169 . T A,G 280.615 G_AF;G_DP AB=0.25,0.75;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1;G_AN=2;G_AF=0.75;G_DP=12;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10
diff -r 7557b71a92e7 -r a6b557df86db test-data/VCFFiltering_input.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/VCFFiltering_input.vcf Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,100 @@
+##fileformat=VCFv4.1
+##fileDate=20140725
+##source=freeBayes v0.9.13-2-ga830efd
+##phasing=none
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
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+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G15_myco
+chr_1 235 . C T 21.392 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865778;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:77:-4.63556,0,-2.351
+chr_1 244 . C T 21.1881 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865718;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-4.61503,0,-2.35102
+chr_1 253 . T C 73.475 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=7.23646;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-8.62509,-0.841726,0
+chr_1 333 . G A 24.2337 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=3.07477;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=82;QR=24;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:24:2:82:-4.69685,0,-1.39164
+chr_1 354 . G A 20.5104 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=2.23682;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=28;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:28:2:78:-4.66174,0,-1.75556
+chr_1 363 . G A 40.3032 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36;MQMR=0;NS=1;NUMALT=1;ODDS=5.91856;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:63:-5.23324,-0.570398,0
+chr_1 1531 . G A 73.2764 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=0;NS=1;NUMALT=1;ODDS=7.23732;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=115;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:115:-9.08235,-0.842098,0
+chr_1 1565 . A G 14.5726 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=38;MQMR=35;NS=1;NUMALT=1;ODDS=3.30493;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=71;RO=2;RPP=7.35324;RPPR=3.0103;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 0/1:4:2:71:2:71:-5.0654,0,-4.84835
+chr_1 1589 . A G 102.964 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55461;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=155;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:155:-10,-1.11316,0
+chr_1 1635 . G A 95.7333 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=38.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55365;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=141;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:141:-10,-1.11274,0
+chr_1 2624 . C T 122.967 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=44.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.5553;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=156;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:156:-10,-1.11346,0
+chr_1 2670 . C T 30.7231 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.739044;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:71:-5.60946,0,-2.40604
+chr_1 2671 . G A 30.0349 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.738983;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:70:-5.5406,0,-2.40606
+chr_1 2686 . A G 28.1218 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.861385;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=39;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:39:2:67:-5.31237,0,-2.3529
+chr_1 2697 . G A 66.8365 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23789;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=104;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:104:-9.39261,-0.842345,0
+chr_1 2699 . G A 75.6507 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23781;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=103;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:103:-9.31979,-0.842311,0
+chr_1 2747 . C T 52.6764 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=5.92179;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=81;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:81:-7.07265,-0.5718,0
+chr_1 3616 . C T 96.527 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55506;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=153;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:153:-10,-1.11336,0
+chr_1 3624 . A G 99.7577 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55532;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=158;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:158:-10,-1.11347,0
+chr_1 3630 . G A 119.888 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=13.8677;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87182;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=191;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:191:-10,-1.38419,0
+chr_1 3657 . T C 146.729 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87224;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:204:-10,-1.38437,0
+chr_1 3681 . C T 141.607 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=8.80089;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=11.1867;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=201;QR=0;RO=0;RPP=8.80089;RPPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:201:-10,-1.65422,0
+chr_1 3746 . G A 143.027 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=177;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:177:-10,-1.38398,0
+chr_1 3766 . TGG TG 207.378 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1M1D1M;DP=7;DPB=4.66667;DPRA=0;EPP=3.32051;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8571;MQMR=0;NS=1;NUMALT=1;ODDS=12.5052;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=267;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=1;SAP=10.7656;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=del;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:267:-10,-1.9258,0
+chr_1 3804 . C T 168.638 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.1667;MQMR=0;NS=1;NUMALT=1;ODDS=11.188;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=213;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=8.80089;SAR=5;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:213:-10,-1.65476,0
+chr_1 3845 . G A 130.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87163;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=184;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=1;SAP=6.91895;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:184:-10,-1.38411,0
+chr_1 3857 . G A 72.7109 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23836;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=113;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:113:-9.98004,-0.84255,0
+chr_1 4299 . C T 48.7928 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=48;NS=1;NUMALT=1;ODDS=2.04069;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=34;RO=1;RPP=9.52472;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:1:34:3:100:-7.69498,0,-2.01683
+chr_1 4311 . A G 138.174 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.8711;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=179;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=3;SAP=3.44459;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:179:-10,-1.38387,0
+chr_1 4357 . C T 141.385 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.87061;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=181;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:181:-10,-1.38366,0
+chr_1 4372 . C T 57.8383 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=48;NS=1;NUMALT=1;ODDS=0.86483;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=40;RO=1;RPP=3.73412;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:1:40:3:110:-8.53351,0,-2.5275
+chr_1 4389 . C T 176.339 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.80219;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=48;NS=1;NUMALT=1;ODDS=6.11702;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=247;QR=37;RO=1;RPP=3.32051;RPPR=5.18177;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:8:1:37:7:247:-10,0,-1.14959
+chr_1 4398 . T C 197.868 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.80219;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=0;NS=1;NUMALT=1;ODDS=12.5039;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=243;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:243:-10,-1.92523,0
+chr_1 4404 . T C 168.543 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=46.3333;MQMR=0;NS=1;NUMALT=1;ODDS=11.1873;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=209;QR=0;RO=0;RPP=4.45795;RPPR=0;RUN=1;SAF=2;SAP=4.45795;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:209:-10,-1.65448,0
+chr_1 4475 . C T 81.0612 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=47;MQMR=0;NS=1;NUMALT=1;ODDS=7.2379;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.86084,-0.842352,0
+chr_1 4540 . C T 72.5101 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23698;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=101;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:101:-9.00573,-0.841952,0
+chr_1 4580 . C T 81.3345 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23817;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=119;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:119:-9.88816,-0.842465,0
+chr_1 4611 . C G 51.9857 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=5.92133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:69:-6.40152,-0.5716,0
+chr_1 4661 . A G 19.7502 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.834078;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-5.08162,0,-2.36476
+chr_1 4678 . G A 21.951 . AB=0.666667;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.136458;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 0/1:3:1:41:2:68:-4.94794,0,-2.78626
+chr_1 4686 . C T 81.6957 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23731;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.44717,-0.842096,0
+chr_1 4699 . G A 103.379 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.55324;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=140;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:140:-10,-1.11256,0
+chr_1 4717 . C T 18.6085 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=34;NS=1;NUMALT=1;ODDS=1.12012;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=40;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:40:2:66:-4.87583,0,-2.24054
+chr_1 4727 . G A 43.4619 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=32;MQMR=0;NS=1;NUMALT=1;ODDS=5.91984;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:66:-5.54913,-0.570955,0
+chr_1 4747 . C T 40.3421 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=5.92045;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:68:-5.83919,-0.571218,0
+chr_1 3305168 . T A,G 280.615 . AB=0.75,0.25;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1 GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10
+chr_1 3305169 . T A,G 280.615 . AB=0.25,0.75;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1 GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10
diff -r 7557b71a92e7 -r a6b557df86db test-data/chr17.VCF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr17.VCF Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,21 @@
+##fileformat=VCFv4.1
+##fileDate=20140725
+##source=freeBayes v0.9.13-2-ga830efd
+##reference=exmple.fsa
+##phasing=none
+##DetectedFormat=freebayes
+##FILTER=
+##FILTER=
+##FILTER=
+##FILTER=
+##FILTER=
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT V1
+chr_17 17 . A G 529.213 G_AF;G_DP AB=0.583333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=21;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.1137;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=77.012;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=751;QR=535;RO=15;RPP=5.59539;RPPR=4.31318;RUN=1;SAF=11;SAP=3.1137;SAR=10;SRF=5;SRP=6.62942;SRR=10;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.58;G_DP=36;G_Base=G GT:DP:RO:QR:AO:QA:GL 0/1:36:15:535:21:751:-10,0,-10
+chr_17 37 . C G 1082.38 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=34;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=3.26577;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=48.0391;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1243;QR=0;RO=0;RPP=15.5282;RPPR=0;RUN=1;SAF=18;SAP=3.26577;SAR=16;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=34;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:34:0:0:34:1243:-10,-9.23017,0
+chr_17 40 . T T 825.518 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=29;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=6.67934;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.92992;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1082;QR=178;RO=5;RPP=9.07545;RPPR=13.8677;RUN=1;SAF=13;SAP=3.68421;SAR=16;SRF=5;SRP=13.8677;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.85;G_DP=34;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:34:5:178:29:1082:-10,0,-6.82575
+chr_17 60 . A . 699.741 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=22;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=17.2236;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=32.2544;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=823;QR=0;RO=0;RPP=9.32731;RPPR=0;RUN=1;SAF=12;SAP=3.40511;SAR=10;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=22;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:22:0:0:22:823:-10,-5.98732,0
+chr_17 73 . T . 846.299 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=27;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=16.6021;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=38.84;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1002;QR=0;RO=0;RPP=5.02092;RPPR=0;RUN=1;SAF=21;SAP=21.1059;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=27;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:27:0:0:27:1002:-10,-7.34226,0
+chr_17 81 . C T 764.464 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=25;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=13.5202;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=36.1324;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=902;QR=0;RO=0;RPP=3.79203;RPPR=0;RUN=1;SAF=19;SAP=17.6895;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=25;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:25:0:0:25:902:-10,-6.76842,0
+chr_17 105 . C T 1154 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=37;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.88603;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=52.0047;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1336;QR=0;RO=0;RPP=19.9713;RPPR=0;RUN=1;SAF=23;SAP=7.76406;SAR=14;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=37;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:37:0:0:37:1336:-10,-10,0
+chr_17 112 . G A 1276.25 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=40;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=10.8276;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=55.9501;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1471;QR=0;RO=0;RPP=10.8276;RPPR=0;RUN=1;SAF=26;SAP=10.8276;SAR=14;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=40;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:40:0:0:40:1471:-10,-10,0
+
diff -r 7557b71a92e7 -r a6b557df86db test-data/chr17.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr17.fa Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,3 @@
+>chr_17
+ccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaa
+TACGCGCGCGCCTAACCCTACGACTTTAACCTACTCTAAACTCTCCTACTAGTACGTCTT
diff -r 7557b71a92e7 -r a6b557df86db tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Dec 15 05:35:36 2015 -0500
@@ -0,0 +1,19 @@
+
+
+
+
+
+ https://urgi.versailles.inra.fr/download/gandalf/VCFtools-1.2.tar.gz
+ python setup_VCFtools.py install
+
+ .
+ $INSTALL_DIR
+
+
+ $INSTALL_DIR
+ $INSTALL_DIR/bin
+
+
+
+
+